Biomedical subjects

Genomics

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PubMed1985

Comparison of genomic fragment and clone sequences within a long interspersed repeated sequence of the mouse genome.

The 393bp nucleotide sequence of a HindIII genomic fragment mapping within the major long interspersed repeated sequence family (MIF-1, Bam, L1) of mouse is reported and compared to clone sequences of the same region of this repeated sequence. The consensus of the clone sequences significantly differs from the genomic fragment sequence by additions and deletions that are inconsistent with the physical and biochemical properties of the genomic fragment. While alternative explanations could account for some of these differences, several aspects of the experimental results imply that cloning artifacts contribute to the discrepancies. Despite the differences between the clone and genomic fragment sequences, the biologically interesting features previously noted in clone sequences (promoter-like signals and an open reading frame) are conserved in the genomic fragment sequence.

Animals↗

PubMed1989

Physical and genetic mapping of the Rhodobacter sphaeroides 2.4.1 genome: genome size, fragment identification, and gene localization.

Four restriction endonucleases, AseI (5'-ATTAAT), SpeI (5'-ACTAGT), DraI (5'-TTTAAA), and SnaBI (5'-TACGTA), generated DNA fragments of suitable size distributions for mapping the genome of Rhodobacter sphaeroides by transverse alternating field electrophoresis. AseI produced 17 fragments, ranging in size from 3 to 1,105 kilobases (kb), SpeI yielded 16 fragments (12 to 1,645 kb), DraI yielded at least 25 fragments (6 to 800 kb), and SnaBI generated 10 fragments (12 to 1,225 kb). A total genome size of approximately 4,400 +/- 112 kb was determined by summing the fragment lengths in each of the digests generated by using the different restriction endonucleases. The total genomic DNA consisted of chromosomal DNA (3,960 +/- 112 kb) and the five endogenous plasmids (approximately 450 kb total) whose cognate DNA fragments have been unambiguously identified. A number of genes have been physically mapped to the AseI-generated restriction endonuclease fragments of total genomic DNA by Southern hybridization analysis with either homologous or heterologous specific gene probes or, in the case of several auxotrophic and pigment-biosynthetic mutants apparently generated by Tn5, a Tn5-specific probe. Other genes have been mapped by a comparison with wild-type patterns of the electrophoretic banding patterns of the AseI-digested genomic DNA derived from mutants generated by the insertion of either kanamycin or spectinomycin-streptomycin resistance cartridges. The relative orientations, distance, and location of the pufBALMX, puhA, cycA, and pucBA operons have also been determined, as have been the relative orientations between prkB and hemT and between prkA and the fbc operon.

Chromosome Mapping↗

PubMed1976

Structure of Herpesvirus saimiri genomes: arrangement of heavy and light sequences in the M genome.

Herpesvirus saimiri contains two species of DNA molecules. (i) The M genome is composed of 70% light (L) DNA (36% cytosine plus guanine; density in CsCl, 1.695 g/ml), which consists of unique sequences, and 30% heavy (H) DNA (71% cytosine plus guanine; density, 1.729 g/ml). (ii) The H genome contains heavy sequences exclusively. H sequences in M and H genomes cross-hybridize completely and are cleaved identically by restriction endonuclease R-Sma I into four classes of fragments with molecular weights of about 360,000, 300,000, 130,000 and 40,000, respectively. H sequences are chains of identical repeat units in tandem arrangement. The molecular weight of each repeat unit is about 830,000. L sequences have no cleavage site for endo R-Sma I H sequences are terminally arranged at both ends of the M genome, as seen by electron microscopy after partial denaturation. The length of the individual heavy ends varies between 21 mum and less than 1 mum, whereas the light region is uniform in size (35.3+/-0.35 mum). As a rule, molecules with a long heavy end at one side have a short heavy end at the other side, thus giving rise to a limited size heterogeneity. Orientation of M DNA molecules by the denaturation map of the light region shows that the longer heavy end may be located at the left or at the right side of the M genome.

Base Sequence↗

PubMed1985

The alpha sequence of the cytomegalovirus genome functions as a cleavage/packaging signal for herpes simplex virus defective genomes.

Although herpes simplex virus (HSV) 1 and human cytomegalovirus (CMV) differ remarkably in their biological characteristics and do not share nucleotide sequence homology, they have in common a genome structure that undergoes sequence isomerization of the long (L) and short (S) components. We have demonstrated that the similarity in their genome structures extends to the existence of an alpha sequence in the CMV genome as previously defined for the HSV genome. As such, the alpha sequence is predicted to participate as a cis-replication signal in four viral functions: (i) inversion, (ii) circularization, (iii) amplification, and (iv) cleavage and packaging of progeny viral DNA. We have constructed a chimeric HSV-CMV amplicon (herpesvirus cis replication functions carried on an Escherichia coli plasmid vector) substituting CMV DNA sequences for the HSV cleavage/packaging signal in a test of the ability of this CMV L-S junction sequence to provide the cis signal for cleavage/packaging in HSV 1-infected cells. We demonstrate that the alpha sequence of CMV DNA functions as a cleavage/packaging signal for HSV defective genomes. We show the structure of this sequence and provide a functional demonstration of cross complementation in replication signals which have been preserved over evolutionary time in these two widely divergent human herpesviruses.

Animals↗

PubMed1987

The 160,000-Mr virion protein encoded at the right end of the herpesvirus saimiri genome is homologous to the 140,000-Mr membrane antigen encoded at the left end of the Epstein-Barr virus genome.

The sequence of 4.4 kilobase pairs (kbp) from the conventional right terminus of the A + T-rich light-DNA (L-DNA) sequences of the herpesvirus saimiri (HVS) genome contains a leftward-directed open reading frame (ORF) for a 1,299-residue protein. The molecular weight predicted for the protein (143,000) is in good agreement with the estimates of 150,000 to 160,000 for the major nonglycosylated polypeptide of the virion tegument (the 160K polypeptide), previously shown to be encoded by this region of the genome. The first initiation codon of the ORF is only 250 nucleotides from the junction of the L-DNA component with the G + C-rich terminal reiterations (i.e., heavy or H-DNA) of the genome. An unusually A + T-rich sequence (43 of 45 nucleotides are A or T, relative to a mean composition of 40% G + C for the ORF) occurs some 75 bp 5' to this initiation codon, and the first adenylation signal (AATAAA) on this DNA strand occurs 18 bp 3' to the termination codon. The amino acid sequence predicted for the 160K protein of HVS is homologous over most of its length to the 1,318-residue protein encoded by the leftmost major ORF of the G + C-rich genome of Epstein-Barr virus (BNRF1, the 140K nonglycosylated membrane antigen). No homology to either of these proteins is evident among the products predicted from the complete sequence of the alpha herpesvirus varicella-zoster virus. Thus gamma herpesviruses with coding sequences which differ in mean nucleotide composition by some 20% G + C have homologous proteins encoded at similar positions with respect to genome termini, with the right end of HVS being homologous to the left end of Epstein-Barr virus.

Amino Acid Sequence↗

PubMed2026

Complete genome of multiply antibiotic resistant ST10 Acinetobacter baumannii isolate NL6 from Vietnam and relationship to available ST10 genomes.

The genome of NL6, a multiply antibiotic-resistant Acinetobacter baumannii ST10:KL49:OCL2 carriage isolate from Vietnam, was sequenced using Nanopore technology, and complete chromosome and plasmid sequences were assembled from the long reads and available short reads. Resistance genes and their locations were identified, and transfer of a conjugative plasmid carrying several resistance genes into a new host was tested. The acquired resistance genes in NL6 were distributed between the chromosome and two of three plasmids present. The chromosome carries multiple copies of several insertion sequences, an incomplete copy of the ISAba1-bounded Tn6250 that includes the sul2 and strAB genes, and an integrative element carrying copper resistance genes designated IECuR. Plasmid pNL6-2 (r3-T5; 15 Kbp) is a Rep_3/OrfX plasmid that includes a tet39 dif module, and pNL6-3 (r3-T20; 66.9 Kbp) carries aacC2d, aphA6, and blaCARB-16 and a second ampC gene preceded by an ISAba1. Conjugation of pNL6-3 into derivatives of ATCC17978 was demonstrated, confirming that the ampC gene confers resistance to third-generation cephalosporins. NL6 was compared to other complete ST10 genomes. Several acquired elements in the chromosome were shared with the ST10 isolate LAC-4 (USA), indicating shared ancestry, but the plasmid content differed. The KL and plasmid content were variable in 17 further complete ST10 genomes downloaded from GenBank. Tn6250 and IECuR were only found together in the chromosome of two further KL49 isolates. Antibiotic resistance in ST10 A. baumannii was acquired mainly via plasmid acquisition, but resistance genes varied, and a variety of plasmids was involved.IMPORTANCEMembers of the CC10 clonal complex of Acinetobacter baumannii comprising ST10 plus single and double locus variants are known to be particularly virulent. However, antibiotic resistance in members of this group has rarely been examined. Here, determination of the complete genome (chromosome and plasmids) of a representative ST10 isolate from Vietnam allowed the context and location of acquired antibiotic resistance genes and of other mobile genetic elements to be determined. Mobile genetic element locations in completed chromosomes facilitate comparisons of potentially related genomes, revealing those with recent shared ancestry. Differences in plasmid content can also be examined.

Acinetobacter baumannii↗

PubMed2026

Genomic Insights Into Multidrug-Resistant Foodborne Serratia liquefaciens Strains Carrying mcr-9 and Comparative Genomic Analysis of Novel Biosynthetic Gene Clusters.

Serratia liquefaciens is an opportunistic nosocomial pathogen with a wide range of antibiotic resistance patterns. This study reports the characterization of the first mcr-9-positive S. liquefaciens strains, 35E-19E1 and CST-066, isolated from meat products in Japan. The strains were screened for the presence of β-lactamases, plasmid-mediated mobile colistin resistance (mcr) genes, and carbapenemase-encoding genes using PCR. Antimicrobial susceptibility was tested using the broth microdilution method. The strains exhibited multidrug resistance (MDR) phenotypes to third-generation cephalosporins, cephamycin, fosfomycin, and other clinically important antimicrobials. Genomic DNA sequencing showed that the genome sizes of CST-066 and 35E-19E1 are 5,529,704 and 5,261,506 bps, respectively. mcr-9 was identified on a chromosome within a genetic environment that included the two-component system qseBC, which plays a key role in the signaling network that triggers colistin resistance in Enterobacterales. Downstream genome analysis revealed a 1695-bp eptB-like kdo2-lipid phosphoethanolamine transferase, which is involved in intrinsic polymyxin resistance mechanisms in Serratia spp. The strain 35E-19E1 carries five CRISPR-Cas enzymes that are essential for adaptive immunity in bacteria, allowing defense against invading elements. Functional analysis using subsystem technology revealed that both strains possess subsystem features responsible for invasion and adhesion within the host biomes. Genome mining using antiSMASH and BAGL4 revealed various biosynthetic gene clusters, responsible for secondary metabolite synthesis. Notably, we identified novel gene clusters, mainly nonribosomal peptide synthetases, in both the strains, indicating their potential to produce bioactive compounds. Although the presence of mcr-9 in Serratia may not be of clinical significance because of natural resistance of the strain to polymyxins, we shed light on the genomic characteristics of this MDR pathogen and the potential spread of mcr-9 among other bacterial species. The emergence of mcr-9 in drug-resistant S. liquefaciens provides significant insights, underscoring the need for increased surveillance of this pathogen.

biosynthetic gene cluster↗

PubMed2026

Pinpointing genomic regions conferring herbicide tolerance in cassava via genome-wide association mapping.

Cassava (Manihot esculenta Crantz) is a tropical crop of major socioeconomic importance, whose productivity can be limited by sensitivity to herbicides used for weed management. This study aimed to perform a genome-wide association study (GWAS) in 194 cassava genotypes to identify genomic regions associated with tolerance to the herbicides mesotrione, S-metolachlor, and chloransulam-methyl. The evaluations performed at 3, 6, 9, 15, and 30 days after application (DAA) were used to characterize the temporal progression of phytotoxicity. Based on this analysis, the phenotype obtained at 9 days after application (PhytoX9DAA) was selected for genome-wide association analyses because it represented the period of greatest symptom expression and the highest discrimination among genotypes. GWAS analyses were performed using de-regressed BLUPs and the MLM, MLMM, and BLINK models, incorporating kinship (K) and population structure (Q) matrices. Significant markers were detected across multiple chromosomes, and the corresponding genomic windows contained candidate genes with functional annotations related to herbicide response. The predominant functional categories included membrane transport, channel activity, signal peptide processing, protein phosphorylation, cellular signaling, and metabolic regulation. Key candidate genes included Manes.02G151900 and Manes.02G152700 (chromosome 2), associated with transmembrane transport and signal peptide processing; Manes.09G060900 (chromosome 9), associated with protein kinase activity, ATP binding, and protein phosphorylation; and Manes.15G083800 and Manes.15G084000 (chromosome 15), associated with S-adenosylmethionine-dependent methyltransferase activity, membrane-related functions, and protein phosphorylation. These genes participate in biochemical pathways involved in cellular signaling, membrane transport, and metabolic regulation that may contribute to herbicide tolerance. Overall, the results demonstrate that herbicide tolerance in cassava is a quantitative and polygenic trait governed by numerous small-effect loci. The integration of cellular signaling, metabolic regulation, and membrane transport supports the physiological resilience of the species under chemical exposure, providing valuable insights for breeding strategies and marker-assisted selection.

Genome-Wide Association Study↗

PubMed2024

The "genetic test request": A genomic stewardship intervention for inpatient exome and genome orders at a tertiary pediatric hospital.

PURPOSE: Exome sequencing (ES) and genome sequencing (GS) are useful tests to diagnose rare diseases in pediatric patients in critical care settings. Genomic test stewardship can increase the appropriate use of these tests leading to improved diagnostics and cost savings. METHODS: A mandatory review of ES and GS orders for admitted patients was implemented in March 2023. Outcomes of the reviews, cost analysis, and subsequent test results through February 2024 were analyzed with descriptive statistics. RESULTS: There were 444 genetic test request orders placed for 412 unique patients. Of these, 81 (18.2%) were redirected and 57 (12.8%) required modification after approval, leading to an overall cost savings of $345,821.00 or $778.88 per order. The combined diagnostic rate was 28.2% in this patient population. CONCLUSION: Stewardship of ES/GS orders for pediatric inpatients is an effective tool to improve the appropriate usage of these genomic tests. Additional collaboration with stakeholders and expansion of genomic stewardship initiatives may shorten the diagnostic odyssey for critically ill pediatric patients and result in cost savings.

Humans↗

PubMed2025

Robust and accurate Bayesian inference of genome-wide genealogies for hundreds of genomes.

The Ancestral Recombination Graph (ARG), which describes the genealogical history of a sample of genomes, is a vital tool in population genomics and biomedical research. Recent advancements have substantially increased ARG reconstruction scalability, but they rely on approximations that can reduce accuracy, especially under model misspecification. Moreover, they reconstruct only a single ARG topology and cannot quantify the considerable uncertainty associated with ARG inferences. Here, to address these challenges, we introduce SINGER (sampling and inferring of genealogies with recombination), a method that accelerates ARG sampling from the posterior distribution by two orders of magnitude, enabling accurate inference and uncertainty quantification for hundreds of whole-genome sequences. Through extensive simulations, we demonstrate SINGER's enhanced accuracy and robustness to model misspecification compared to existing methods. We demonstrate the utility of SINGER by applying it to individuals of British and African descent within the 1000 Genomes Project, identifying signals of population differentiation, archaic introgression and strong support for ancient polymorphism in the human leukocyte antigen region shared across primates.

Humans↗

PubMed2025

Streamlining large-scale genomic data management: Insights from the UK Biobank whole-genome sequencing data.

Biobank-scale whole-genome sequencing (WGS) studies are increasingly pivotal in unraveling the genetic bases of diverse health outcomes. However, managing and analyzing these datasets' sheer volume and complexity presents significant challenges. We highlight the annotated genomic data structure (aGDS) format, substantially reducing the WGS data file size while enabling seamless integration of genomic and functional information for comprehensive WGS analyses. The aGDS format yielded 23 chromosome-specific files for the UK Biobank 500k WGS dataset, occupying only 1.10 tebibytes of storage. We develop the vcf2agds toolkit that streamlines the conversion of WGS data from VCF to aGDS format. Additionally, the STAARpipeline equipped with the aGDS files enabled scalable, comprehensive, and functionally informed WGS analysis, facilitating the detection of common and rare coding and noncoding phenotype-genotype associations. Overall, the vcf2agds toolkit and STAARpipeline provide a streamlined solution that facilitates efficient data management and analysis of biobank-scale WGS data across hundreds of thousands of samples.

Humans↗

PubMed2025

Delivering effective genome sequencing in pediatric care: From research in the 100,000 Genomes Project to routine clinical practice.

PURPOSE: Genome sequencing (GS) is increasingly used to investigate rare conditions, primarily in children. The 100,000 Genomes Project (100KG) evaluated GS ahead of implementation in the English National Health Service. In 2020, the National Health Service Genomic Medicine Service (GMS) became the first public health care system to offer GS in routine clinical care. We investigate how learning from 100KG informed GMS service delivery. METHODS: We compare GS outcomes in children tested at a large pediatric hospital via GMS (n = 501) and 100KG research (n = 1759). RESULTS: GMS diagnostic yield (29%) was higher than that in 100KG (22%) (P < .0016). Median age at testing was 8 years in 100KG and 6 in the GMS (P < .05). In 100KG, the diagnostic yield was <10% for 15 indications, none of which are included in GMS testing. 100KG data showed little benefit to application of >3 panels. Use of fewer but larger GMS panels resulted in a significantly higher number of genes tested per patient: median 2801 vs 1373 in 100KG (P < .001). In 100KG, diagnostic yield was not significantly increased by testing more than 3 family members (n = 34/142, 24%). CONCLUSION: Learning from 100KG has informed GS clinical service delivery, resulting in higher diagnostic yields and earlier age at testing. Lessons are broadly applicable to all services providing GS, enabling earlier access to tailored management with fewer investigations.

Humans↗

PubMed1992

The Taiwanese hepatitis C virus genome: sequence determination and mapping the 5' termini of viral genomic and antigenomic RNA.

The complete nucleotide sequence of hepatitis C virus (HCV) cloned from the liver tissue of a Taiwanese patient with post-transfusion type C hepatitis was determined. The 5' end of HCV genomic RNA was located 341 nucleotides upstream from the initiation codon for the viral polyprotein open reading frame. The 5' end of the viral antigenomic RNA was shown to have 13 consecutive As. Thus the 3' terminus of the viral genome is a stretch of U which ends about 50 nucleotides downstream from the stop codon of the large open reading frame. The nucleotide sequence homology between this HCV strain and two Japanese isolates was 90.5 and 90.7%, respectively. Homology with the United States strain, however, was only 77.8%. Accordingly, the indigenous Taiwanese HCV strain is of the same subtype as the Japanese isolates. Novel features of the viral genome termini are possibly relevant to HCV genome replication.

Amino Acid Sequence↗

PubMed1992

Nucleotide sequence of the genome of the bacteriophage alpha 3: interrelationship of the genome structure and the gene products with those of the phages, phi X174, G4 and phi K.

The complete nucleotide sequence of the genome of the circular single-stranded DNA (isometric) phage alpha 3 has been determined and compared with that of the related phages phi X174 and G4. The alpha 3 genome consists of 6087 nucleotides, which is 701 nucleotides longer than the nucleotide sequence of the phi X174 genome and 510 nucleotides more than that of the G4 genome. The results demonstrated that the three phage species have 11 homologous genes (A, A*, B, C, K, D, E, J, F, G and H), the order of which is fundamentally identical, suggesting that they have evolved from a common ancestor. The sequence of some genes and untranslated intergenic regions, however, differs significantly from phage to phage: for example, the degree of amino acid sequence homology of the gene product is averaged at 47.7% between alpha 3 and phi X174 and 46.9% between alpha 3 and G4, and alpha 3 has a remarkable longer intergenic region composed of 758 nucleotides between the genes H and A compared with the counterparts of phi X174 and G4. Meanwhile, in vivo experiments of genetic complementation showed that alpha 3 can use none of the gene products of phi X174 and G4, whereas the related phage phi K can rescue alpha 3 nonsense mutants of the genes B, C, D and J. These sequencing and in vivo rescue results indicated that alpha 3 is closely related to phi K, but distantly remote from phi X174 or G4, and supported an evolutional hypothesis which has been so far proposed that the isometric phages are classified into three main groups: the generic representatives are phi X174, G4 and alpha 3.

Amino Acid Sequence↗

PubMed2026

Folding a broken genome: the versatile roles of cohesin in genome maintenance.

Cohesin is a protein complex that shapes 3D genome organization through two distinct mechanisms. First, cohesin tethers replicated chromatids from DNA replication until mitosis. This process, known as sister chromatid cohesion, ensures accurate chromosome segregation and enables high-fidelity DNA repair through homologous recombination between the sister chromatids. Second, cohesin organizes the genome during interphase by dynamically extruding chromatin loops, structures that have key roles in gene regulation. Recent work has shown that, in addition to the well-established repair functions of sister chromatid cohesion, cohesin-mediated chromatin looping is closely linked to the repair of DNA double-strand breaks - one of the most toxic DNA lesions. In this Review, we discuss the central roles of cohesin in maintaining genome stability, with emphasis on the cellular response to DNA double-strand breaks. We review how dynamic loop structures facilitate signalling of repair events and promote long-range chromatin motions that underpin the repair process. Overall, its dual mode of action - cohesion and loop extrusion - positions cohesin as a central regulator of chromatin architecture and genome maintenance.

Cohesins↗

PubMed1990

Towards a physical map of the Drosophila melanogaster genome: mapping of cosmid clones within defined genomic divisions.

A physical map of the D. melanogaster genome is being constructed, in the form of overlapping cosmid clones that are assigned to specific polytene chromosome sites. A master library of ca. 20,000 cosmids is screened with probes that correspond to numbered chromosomal divisions (ca. 1% of the genome); these probes are prepared by microdissection and PCR-amplification of individual chromosomes. The 120 to 250 cosmids selected by each probe are fingerprinted by Hinfl digestion and gel electrophoresis, and overlaps are detected by computer analysis of the fingerprints, permitting us to assemble sets of contiguous clones (contigs). Selected cosmids, both from contigs and unattached, are then localized by in situ hybridization to polytene chromosomes. Crosshybridization analysis using end probes links some contigs, and hybridization to previously cloned genes relates the physical to the genetic map. This approach has been used to construct a physical map of the 3.8 megabase DNA in the three distal divisions of the x chromosome. The map is represented by 181 canonical cosmids, of which 108 clones in contigs and 32 unattached clones have been mapped individually by in situ hybridization to chromosomes. Our current database of in situ hybridization results also includes the beginning of a physical map for the rest of the genome: 162 cosmids have been assigned by in situ hybridization to 129 chromosomal subdivisions elsewhere in the genome, representing 5 to 6 megabases of additional mapped DNA.

Animals↗

PubMed1992

Hepatitis C virus (HCV) circulates as a population of different but closely related genomes: quasispecies nature of HCV genome distribution.

Sequencing of multiple recombinant clones generated from polymerase chain reaction-amplified products demonstrated that the degree of heterogeneity of two well-conserved regions of the hepatitis C virus (HCV) genome within individual plasma samples from a single patient was consistent with a quasispecies structure of HCV genomic RNA. About half of circulating RNA molecules were identical, while the remaining consisted of a spectrum of mutants differing from each other in one to four nucleotides. Mutant sequence diversity ranged from silent mutations to appearance of in-frame stop codons and included both conservative and nonconservative amino acid substitutions. From the relative proportion of essentially defective sequences, we estimated that most circulating particles should contain defective genomes. These observations might have important implications in the physiopathology of HCV infection and underline the need for a population-based approach when one is analyzing HCV genomes.

Amino Acid Sequence↗

PubMed1991

[Features of genome expression of phage transposon D3112 of Pseudomonas aeruginosa in Escherichia coli bacteria: dependence of bacterial phenotype on copy number of D3112 genome].

Escherichia coli (RP4 :: D3112) bacteria manifest Tcs phenotype (thirty centigrade sensitivity), i.e. the cells do not divide and form colonies under conditions of lowered temperature (30 degrees C and lower), while cells grow normally at 42 degrees C. In this work it is demonstrated that replication-transposition of D3112 and the Tcs phenotype depend on no recA system of E.coli. Following events lead to the loss of the Tcs phenotype (in E.coli (RP4 :: D3112) cells survived after growing at 30 degrees C): occurrence of mutations in bacterial, phage and plasmid genomes, elimination of DNA of hybrid plasmid or RP4 DNA (a portion of DNA) as well as integration of the hybrid plasmid into bacterial chromosome. In the latter case, the E.coli (D3112) cells acquired the properties shared by the initial bacteria and those with the Tcs phenotype. Such clones are designated tcl (thirty centigrade low sensitivity), they are able to form colonies at 30 degrees C but their growth is more slow, they maintain instability at lowered temperature and continue to produce D3112 phage. The tcl clones in which replication-transposition of D3112 DNA in less effective than in the tcs clones are a suitable object for the study of genetic rearrangements caused by D3112 phage transposon. It is shown that either complete RP4 genome or its portion are comprised between direct repeats of D3112 and are built into various chromosomal sites, i.e. cointegrates are being formed. Two types of deletions are revealed: eliminating sites of RP4 plasmid adjacent to the left end of D3112 genome as well as deletions of the D3112 genome. It is demonstrated that alteration in the growth nature of E.coli, carrying D3112 DNA, at 30 degrees C depends on the copy number of D3112 per bacterial cell.

Bacteriophages↗